Mysteries of the Unknown
by true2love
Summary: Based on the Sonic the Hedgehog Next-Gen (2006)'s Team Dark or Shadow's storyline. Chapter for every stage. The complicated life of Shadow the Hedgehog, Rouge the Bat, and E-123 Omega as they uncover the truth about Mephilis the Dark, the two newcomers from the future, Silver and Blaze, and the truth of the ill-fated black hedgehog. Shadow & Rouge-ness, Team Dark-ness


**Hello everyone! ^^**

**All my current followers as of July the 2nd, 2013 I guess are following me because of my Tales of Symphonia fanfics. But I've always wanted to wright a Sonic one, or more specifically, a Shadow&Rouge one. ^^**

**I'm kinda following the Sonic Next-Gen story (because honestly, Team Dark has a great story in this) so here's the story. Starting in White Acropolis, read and have fun! ; )**

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**STAGE 1:**

_**White Acropolis**_

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"Damn it," she cursed as she found yet another exit to the Doctor's base heavily guarded by various new models of Eggman's robots.

Quickly spotting a search light rapidly coming her way, G.U.N. agent and spy, Rouge the Bat, returned to the shadows of the mountain. She hadn't done all of this work to be caught now. "This is all your fault!" she angrily told the item she had come to steal as loudly as a whisper could allow her. Her mission had been to retrieve this so called 'Scepter of Darkness' from Eggman's base and bring it to the G.U.N. headquarters. The only real problem had been the security not letting her out. She was certain that she hadn't made any mistakes that could have locked her up, so she assumed it was inevitable. Eggman was smart, and he could certainly learn from his mistakes. Plus, he knew how skilled she was in the art of trickery. She had stolen many things from his bases before, black hedgehog and top E-series robot included, heck, she had even stolen _for_ him. The thought of those enchanting emeralds made her long for an escape even more. She knew then that she wasn't meant to be held captive. She was meant to be free.

She cursed G.U.N. for a moment. She had asked for their help _26 hours ago_! Where _were_ they? She was tired and freezing. She hadn't blinked an eye shut since she had gotten here, which was now almost 30 hours ago, and the entire region was covered in a thick layer of snow. '_They better have a _huge_ pay waiting for me after this, or I swear I'll-!_' Her bitter thoughts were interrupted by a huge explosion at the northern main gate.

She never thought an explosion could bring her so much hope.

She quickly moved to get a better view at what was happening there, while noticing that the search lights did not appear alarmed by what had happen at the gate. She concluded they weren't moved by sound, only visual, because only the two closest to the northern gate shot in the direction of any possible intruders. '_Who could be so…'_ she didn't want to say 'stupid', but 'smart' wasn't the way to describe ones who just barge in through the main gate. She had only managed to get in with every sneaky way possible.

She knew for a fact that G.U.N. never proceeded this way, and certainly never for her. This naturally led her to think of her two teammates. Sure, Sonic and the others could have been responsible for that explosion, but they could never know she was here, and Omega liked blowing stuff up more than anyone.

Then again, her teammates couldn't know her whereabouts either. She didn't even know theirs. They could be halfway across the world for all she knew. And the more she thought about it, the more likely it was Sonic, just coming to trash another one of Eggman's hideouts.

Yes, either that or Eggman suddenly liked blowing his own robots to pieces…

What seemed more likely to you?

Her next move was to reach Sonic, if he was indeed here. Maybe if she was lucky he'd be accompanied by that red echidna. But she hadn't proven herself to be very lucky these past hours had she? Nevertheless, she needed and wanted to get out of here as soon as possible.

After so many hours of travelling, yes, the base was _that _big, she had a fairly good idea of her surroundings, and knew that the base had an inner section and an outer section. She was in the inner section, where she was trapped in. Normally she would have just flown away, but with so many robots and search lights everywhere, she didn't see how she could get far.

Turning back to the gate she had been studying before the explosion, she noticed the robots were heading north, towards the main gate. Maybe she still had a little luck left in her after all. She carefully glided down to the metallic gate while staying away from the search lights. Coming closer, she easily came to the unfortunate conclusion that as long as the security system was up, she was still stuck here.

She kicked the door to vent her ever-growing frustration until she was worn out. She dropped to her knees and rested her hands and head on the cold metallic door. She let out a dry laugh when she remembered she had been in this sort of situation only once before. It had been a more dangerous experience since the island was set to blow up completely with her and three of the Chaos Emeralds on it. He had saved her then, but this time, she didn't have any of the Chaos Emeralds to assure her he'd rescue her again, and she already knew the Scepter of Darkness would be of no interest to him.

She let out a quick sigh and bit her lower lip. He didn't _have _to be so cold.

She shook her head and got up, reminding herself that the black hedgehog did not know where she was, and that she should only depend on him when they were on missions _together_.

Rubbing her arms quickly, she stepped away from the gate, hoping to find any form of help. She didn't go far since it was so hard to walk in all of this snow. Her wings stung of bitter cold so she warped them around her body for a little extra warmth. If only she knew where and how to shut the security system down. She probably could shut it down with ease, but without the location, it was useless.

She heard more explosions in the distance, and soon after she spun to see the gate open.

In a matter of seconds, she was out of the inner section. She quickly looked around, not sure which way to go, until she heard loud metallic sounds coming from her left. It was difficult to see what it was through the snow, but she recognized the flashes of blue light almost instantly.

It was Chaos Control, or a smaller version of it, since she was sure he did not have a Chaos Emerald with him. She would have felt it if he had.

And she doubted Sonic had learned to use it so skillfully in the past five months.

There wasn't anyone else who could perform that. To her, only an ultimate lifeform could.

Another flash of light appeared just a couple feat before her, and sure enough, the black hedgehog himself stood there when the light faded.

"Shadow," she began. She had been so sure he wouldn't or couldn't come, yet her he was. Why was that? "Why you?" She finally asked.

He watched her carefully, as if to study her physical condition, before answering: "It's a request from the President."

"What happened to G.U.N?! I asked for their help - !"

"26.3 hours ago," he completed. "Let's go."

The rescued agent pouted, a little annoyed. "Fine. Warp us out of here."

"Not now," the bat glared at him the second those words left his lips, "My mission is to infiltrate the Doctor's base and retrieve information from his database, we can't leave now," he explained, ignoring her glare while crossing his arms.

"No, Shadow! I'm starved and freezing and tired and I just wanna get the hell out of here!" she almost begged.

A smirk appeared on his lips as he hid a small laugh. That was one of the things she loved about her, well, yes, best friend and teammate. He would never have done that simple action in front of anyone else but her and probably their third teammate, E-123 Omega. Even if it was to hide a laugh, it already brightened her mood. "Being mortal sure has a lot of disadvantages, doesn't it?" he said, as he lost his smirk and turned to scan the surroundings for any incoming robot or search light.

She sighed, a smile gracing her features, "Tell me about it. Let's get this over with so I can go home and take the longest bath in years." He nodded. Rouge had always reclaimed a hot bath after every one of the missions they had been on together. It had become almost a part of a routine to him. "You know, Shadow," he easily recognized her flirtatious voice, for it wasn't new to him either, not that he disliked it, but he sure wasn't going to say anything about it, "my bathtub still fits room for two," she finished by adding a seductive wink.

Like always, he brushed the suggestion aside. "I don't get tired half as easily as you think I do, and showers are more efficient and take less time." He started moving away as he quickly counted the number of search lights within the base.

"Aww, you're no fun. Hey-!" the bat just noticed now that Shadow was walking _on top_ of the snow thanks to his air shoes while she was ankle-deep. Quickly, she cleared her throat and assumed a helpless pose.

Just as planned, Shadow turned to look at her.

"Mind _helping _your damsel in distress?" she said as she placed her hand that held the very item that had got her in this situation to her forehead.

He stared curiously at the Scepter of Darkness in her hand before glancing down at her feet. Indeed, she wouldn't do well on foot. He stared up to her aquamarine eyes, "Did something happen to your wings?" Because, normally she would immediately use her wings when her legs where close to useless. She would even choose them over her feet most of the time. Shadow thought it was understandable. If you had the ability of flight, why settle for the ground?

"Well…" She turned a little to give him a better view of her wings, which were now covered in a coat of frost, "They were cold."

Shadow stepped up to her and grabbed one of her frozen wings. "Hey! Be careful!" she warned him, a little afraid that he might break it or something. She was surprised to feel him handle her wing with care, folding and unfolding it gently. "Then it'll be faster if I carry you, just make sure to move them as much as possible," he lifted her in his arms with ease and skated away.

"Thanks, I wouldn't want to lose them or anything," she told him, but the wind he was making rendered her voice just above a whisper. The wind was soon unbearable to her exposed skin and she demanded that she was put down.

"Ugh! I hate this place so much!" she cried, now shivering uncontrollably. Shadow was looking around again, for what, she had no idea and hadn't a particular care to know.

"Wait here," he told her before skating off to what looked like a military garage of some sort. Soon enough, a military truck thing – she had never been knowledgeable in cars and such – drove right through the thin metallic door. It braked a few feet away from her and the passenger seat door was kicked open by a familiar air shoe.

Shadow got out of the driver seat and walked back to her side. "This'll have to do, now let's go," he said as he gestured the passenger seat. She happily climbed into the truck, but now that she thought about it, it was probably more of a Jeep, although she honestly didn't care at the moment. As soon as she was in, Shadow was already driving at full speed. She searched her seat for a seatbelt, but found none. '_Figures._' At least this vehicle had a closed roof.

She noticed her teammate was pushing buttons on a dash that looked nothing like an ordinary car dash. Something launched from the vehicle and crashed right into one of the search light towers. It came crumbling down in a matter of seconds.

"So this thing has a missile launcher, but does it have a heater?" she asked, wanting to warm her freezing form badly. He glanced at her briefly and pressed a couple extra buttons and warm air enveloped her comfortably.

Time had passed quickly and Shadow had brought the Doctor's defense down easily. He could now get the information on this so-called 'Solaris Project'. He had been ordered to find out exactly what Eggman was up to this time. He expertly parked the military jeep in front of the entrance to the actual base when a thought crossed his mind. Why was Rouge so quiet? She was always the one to fill the silence, and he who regularly enjoyed silence, he still enjoyed to hear Rouge break it time after time. He turned to look at his passenger to find out what was wrong.

To his surprised, she was cuddle up in the seat and sleeping peacefully while clutching the grey scepter that flowed with purple light, despite all of the noise and movement he had been causing just moments ago.

He just stared at her, not sure what to do. '_She really was tired_' he thought and realized this was the first time he had ever seen her sleep. It's not like he normally stuck around long enough to have ever seen her like this before. She was… truly beautiful right now and she seemed to be perfectly graceful even when sleeping. Shadow noticed the frost on her wings and in her hair had melted away and left her body glistering wet, a rather appealing sight indeed. He felt his body change at the sight and quickly looked away. He would never do anything like that to his best and only real friend beside their robot teammate. "Rouge," he attempted to wake her up by shaking her shoulder a bit.

Something proved to wake her up much easier. It was some sort of metallic robot, one of Eggman's, no doubt. His sleeping passenger shot straight up, almost shrieking. The rear view mirror showed a huge four-legged robot running straight at them. "Get inside," Shadow stated his order calmly, "I'll take care of it."

Rouge spun around to see the source of danger and quickly nodded before opening the door and running toward the entrance, where she kicked it open. Meanwhile, Shadow casually backed the car away and proceeded to bombard that thing with his two remaining missiles.

Failing to bring the robot down with only missiles, the hedgehog jumped out of his vehicle just before the beastly robot crushed it with his paw. Shadow noticed it had a collar around its neck that read 'Egg Cerberus'. He dodged another paw and attacked it with Chaos Spear. He didn't like how little damage it was doing, still a smirk stretched across his face. At least Eggman knew how to test him.

"Try the rod on its head!"

The black hedgehog shot a look at the female bat and gestured her to go back inside, back to safety. She gave him an angry look and went back. Nevertheless, Shadow took note of her idea and jumped onto the thing's back and climbed his way to its head. The Egg Cerberus tried to shake him loose by any means possible, fully aware he was very vulnerable now. Shadow held strong and grabbed the rod and yanked it towards the mountain, making the robot helplessly crash into the rocky mountain. Pieces of his armor fell to the snowy ground as it release itself from the mountain. It growled ferociously before attempting to get rid of the hedgehog pest on its head. Shadow simply slammed it into the mountain again and again to remove as much armor as possible. It kept growling furiously at the damned hedgehog. Finally, Shadow leapt off of it, ready for the final blow. The Egg Cerberus conveniently approached the hedgehog as if preparing to pounce on its prey. The Ultimate Lifeform shot a Chaos Spear at what he recognized to be the robot's computer, leaving the robot completely useless. It fell to the ground heavily and that was that.

He found Rouge had already made her way into the base and reached her quickly. She was studying something on the ground. He looked around, finding the interior of the base strange. It was basically just a hallway that led to a dead end, where Rouge was still staring at a circular design on the ground. "It's a transporting device," she concluded, just as Shadow neared her, "I'm sure of it. The same thing was in one of his base within the Pyramid Cave in the desert," she paused, "That one had teleported me directly within the Space Colony Ark."

She looked at him then, memories were rapidly surfacing in her mind. She could only wonder if he still remembered any of what happened before his fall to the earth. Apparently, with the events of the Black Arms he remembered everything, but she had never asked him directly. She had just assumed. What if he didn't remember? She decided to ask.

"How many times have you saved me by now? I've lost track. It must be getting annoying, right?"

He seemed be thinking as he stepped onto the circular design that glowed to his contact, but otherwise did nothing. "How does this work?" he asked her, ignoring her question.

She stayed silent a moment, a little annoyed that he had ignored the question. Did he avoid the question because he didn't know? Shadow interrupted her before she could speak.

"It still gets blurry sometimes," he answered slowly, looking away, "I don't know now, but I know that sometimes I do."

Now she felt guilty. "I'm sorry Shadow," she apologized, "Curiosity got the best of me I guess," she smiled, not letting the mood drop too low. "Now let's see, do you think Eggy made it so only he can use it?" she asked the hedgehog, changing the subject back to the transporter.

"Probably," he answered; after all, Eggman had already proved to have made many improvements on his part.

"Then maybe it's weight-based," she suggested.

Quickly Shadow pulled her closely to him with a hand on her waist, so she could stand on the transporter, something she hadn't first realized as a small blush reached her cheeks. Still, it did not work. "Maybe we could use an object for extra weight?" the bat tried another suggestion. Both of them looked around but there was remotely _nothing_ to use. Cursing loudly, Shadow thought he had used enough of his patience, while Rouge simply gave up. After all, it wasn't _her_ mission, it was his. So she started conversation once again. She had wondered why her teammate hadn't brought the Scepter of Darkness up yet.

"Don't you wanna know what this is?" she asked the hedgehog that was now tearing the metal walls down, probably hoping there would be something of help behind them. His efforts were unsuccessful, _of course_. He slightly turned around to see the scepter she was talking about. His face showed just how annoyed he was about their situation, and she knew he wouldn't care about the thing _now_.

"My assignment was to rescue you, nothing more." He answered before returning to his unsuccessful work.

"Fine," there he went again, "With you it's always business."

The only sound of Shadow tearing down the walls filled the room as Rouge studied the Scepter of Darkness, the item that was still responsible for everything. Staring at it, she found its design very familiar to the one on the transporter. Could they be related somehow? The female agent crouched down to study the transporter's design once again. Sure enough, there was a small circle the exact size of the scepter's diameter. Wasting no more time, she stuck the scepter into the circle and disappeared through glowing pink rings.

"Rouge!" Shadow spun around as soon as he heard she was gone through the transporter. He was standing next to it, wondering where she had gone. He didn't have to worry long, for pink glowing rings reappeared along with the bat.

"What would you do without me, Shadow?" she flattered herself as she brushed a hand through her hair, wearing a teasing smirk.

He said nothing, but he wore a small smirk of his own and stepped onto the transporter with her. Rouge placed the scepter correspondingly and they both vanished within pink glowing rings.

They reappeared in a room that still resembled Eggman's many bases. There was a huge digital screen with a wide keyboard under it. It was Eggman's main computer, no doubt. The two looked around, taking a couple steps forward. Rouge was already studying the map shown on the screen while Shadow scanned the area for any source of danger. Finding none, he returned is attention to the screen as his teammate reached a conclusion. "Ah, Soleanna, the city of water," she began as she recognized the city, and continued with information she knew about the place, "It has a constitutional monarchy, you know," Shadow turned to a painting hanging on the wall, already uninterested as the female bat continued, " The primary industries tourism and crafting precision machinery." She stopped to watch the painting Shadow was now walking to, "The current sovereign is Princess Elise The Third," she explained the girl on the portrait, finally making Shadow speak again.

"Why does Eggman's base lead to an odd place like this?" He asked her as he turned to face her.

She shrugged, "How should I know? I just followed my orders and retrieved the item," she answered, toying with the mysterious scepter in her hands.

"Anyway," she added before turning back to the computer screen and pressed a few keys, "I have a little favor to ask of you," the map focused on a larger image of the outer area of Soleanna. Shadow stepped closer to the screen, signaling her to go on. "Could you escort me to the G.U.N. rendezvous point?" she asked him as her eyes left the screen to meet his. She watched him stay silent a bit before he finally spoke.

"Where's the rendezvous point?"

She smiled. If he bothered asking where it was, that meant he intended to help her. For once, maybe they could work together for longer than 'just business'. "It's the ancient castle of Soleanna," she answered, pointing the spot on the map, "in Kingdom Valley."

"Fine, but first, find everything there is on the Solaris Project in the Doctor's computer," he told her while crossing his arms.

"What? But that's your job!" she complained, "And I'm not exactly at top shape right now, you know," she made sure to add. Certainly _he_ wasn't the one who's been stuck here in this freezing prison with no food or sleep for so long. She had absolutely _no _desire to know how long it had been. Shadow simply 'hmphed' and approached the keyboard. Rouge watched him remain emotionless as he tried a few keys that ultimately led him nowhere in his search of information on the Solaris Project. It made her realize how _tired_ she was of being here and how _faster_ it'd be if _she_'d hack the computer instead of him. After all, she was both a G.U.N. agent and _spy_, while he was only an agent; an excellent one, she had to admit, but a new one nevertheless. Both the President and the G.U.N. Commander had requested Shadow a few weeks later after the whole Black Arms incident. She smiled to herself then, remembering how she would always find him cleaning up the mess Black Doom and the Black Arms he came across, which was everywhere. He had told her then that it was the least he could do after what he blamed to be his entire fault. There wasn't much she could say then to cheer him up. Then again, when had she actually managed to cheer him up?

Her smile faded.

She forced that thought away. She had stayed by his side then, and had made the decision to stay by his side from then on. Whether she'd word her decision to him was another matter. Maybe she was waiting for the right opportunity? Anyway, she had cleared her share of black aliens for him then, she could certainly hack a stupid computer now.

Rouge stepped closer to the keyboard also, while slightly pushing the black hedgehog aside before he got too impatient with this piece of technology. He let out a breath and step quietly back, letting her work. Of course he was thankful, but he wasn't one to openly thank everyone for everything, and he knew she knew that. So it wasn't a problem… was it?

After a few minutes, his female partner concluded that data on the Solaris Project was either impossible to find or wasn't there. She added how Eggman had already proved that he could outsmart her skills as a spy.

"Then our work is done," he concluded also as he took out what Rouge recognized as a time bomb and set it on the computer screen. "Let's get out of here," he told her as he walked back to the transporter and waited for her.

"Right," she answered, hurrying to his side. The memories of the last time he had set off this sort of device surface in her mind. Thank goodness Shadow came back for her then.

She quickly placed the Scepter of Darkness in place and they were teleported back into the corridor. As soon as they were out of the building, Shadow teleported away, leaving an unfazed Rouge in the cold. He hadn't gone through the trouble of saving her only to leave her behind. She wasn't worried.

Surely, she heard the sound of an engine and recognized the same vehicle that had brought her here. Shadow kicked the passenger seat door open and she quickly got in. They drove away until they stopped on safe, higher ground. "Now watch for fireworks," the bat said as she crossed her arms behind her head and leaned in the seat.

Shadow watched her relax in her seat, something she hadn't done for what he guessed to be a few days perhaps. He thought he felt reassured that she could now do so and returned his gaze towards the base that had just started to blow up. Rouge laughed a little while watching their so-called fireworks, making Shadow's eyes return to her. "Omega would've loved this," she said.

The ebony hedgehog smiled back at the explosion. "I'm sure he would," he agreed.

After that, Rouge had only asked to be taken home. Unfortunately, Shadow had orders to bring her and himself back to the G.U.N. headquarters, and she could argue all she liked, Shadow was bringing her there and that was that.

The drive there was a long one though, and Rouge had fallen asleep again. After cursing a bit to himself, Shadow concluded that she wouldn't be in any shape to speak with the Commander now… …and Night Babylon wasn't too far away…

He looked at her sleeping form and rolled his eyes at how easily his mind was made up when he looked at her. He drove south, away from the G.U.N. headquarters. He'd take her home, to Club Rouge.

He didn't remember how long it had been since the last time he had been at her place, this flashy neon club she called home. He remembered the first time he had laid eyes on the place, all the dancing lights had reminded him so much of the billions of stars he could see from the Ark. Stepping foot inside, the loud music and energy vibrating among the crowd almost attacked him. Taken aback, he had immediately returned outside. The view of Night Babylon may have reminded him of the Ark, but Rouge's club was nothing like it. The Ark was always silent and still, so much that he knew that if it weren't for Maria, he would never had been happy there. That's when he realised that this attractive bat would bring life to his monotonous immortality. Whether he'd want it or not was another story.

Thinking about that now as he parked the car on the side of the street, he realized that if he was even still around her now, after all those years, it meant that he wanted her to light up his days.

He picked her up and chaos controlled inside her apartment on the upper floor of Club Rouge. Rouge's bedroom was up another small set of stairs. There was no door to her room, only a dark violet curtain. Shadow pushed the cloth aside and stepped in the hexagonal-shaped room, the perfect shape of a diamond. On his left was a single wide window, the only source of light, and even it was covered with thick black and purple curtains. It wasn't new information to Shadow that Rouge, being the mysterious bat she was, was no fan of strong lighting, something he could honestly relate to.

He laid her on her bed in the middle of the room. He didn't go as far as to place her under the covers. He thought it inappropriate; she was no child who needed to be tucked in. She was a strong and independent, not to mention _beautiful_, woman. She didn't need his care.

Stepping away, he gazed at her shortly before pressing a button hidden under one of the wooden planks on the floor. She had showed it to him around two months ago

That's when the sealing above her bed in the shape of a circle opened to reveal a sky of diamonds that glimmered across her features. In his eyes, it looked like stars where shinning down upon her.

The strange feelings crawled back around his heart and he knew he had to leave.

And so he chaos controlled away.

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**THE END :D**

**Nah, I'm kidding.**

**I'll try writing a chapter for every stage. (Can't promise an expected date, but chapter 2 is already in process, so hopefully, soon)**

**Don't forget to review please = )**


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